Merge branch 'master' into cornu/add_eigen

.github/workflows/neuron-ci.yml

@@ -27,7 +27,7 @@ jobs:
 
     name: ${{ matrix.os }} - ${{ matrix.config.build_mode }} (${{ matrix.config.cmake_option }}${{ matrix.config.config_options }}${{ matrix.config.matrix_eval }}${{ matrix.config.sanitizer }})
 
-    timeout-minutes: 45
+    timeout-minutes: 75
 
     env:
       INSTALL_DIR: install

src/neuron/container/node.hpp

@@ -244,9 +244,13 @@ struct handle_interface: handle_base<Identifier> {
     }
 
     friend std::ostream& operator<<(std::ostream& os, handle_interface const& handle) {
-        return os << "Node{" << handle.id() << '/' << handle.underlying_storage().size()
-                  << " v=" << handle.v() << " area=" << handle.area() << " a=" << handle.a()
-                  << " b=" << handle.b() << " d=" << handle.d() << '}';
+        if (handle.id()) {
+            return os << "Node{" << handle.id() << '/' << handle.underlying_storage().size()
+                      << " v=" << handle.v() << " area=" << handle.area() << " a=" << handle.a()
+                      << " b=" << handle.b() << " d=" << handle.d() << '}';
+        } else {
+            os << "Node{null}";
+        }
     }
 };
 }  // namespace neuron::container::Node

src/neuron/container/non_owning_soa_identifier.hpp

@@ -69,13 +69,6 @@ struct non_owning_identifier_without_container {
         return !m_ptr;
     }
 
-    /**
-     * @brief Get the underlying pointer value.
-     */
-    [[nodiscard]] std::size_t* get_raw_pointer() const {
-        return m_ptr;
-    }
-
     friend std::ostream& operator<<(std::ostream& os,
                                     non_owning_identifier_without_container const& id) {
         if (!id.m_ptr) {

src/neuron/container/soa_container.hpp

@@ -765,6 +765,16 @@ struct soa {
         return result;
     }
 
+    void shrink_to_fit() {
+        if (m_frozen_count) {
+            throw_error("shrink() called on a frozen structure");
+        }
+        for_each_vector<detail::may_cause_reallocation::Yes>(
+            [](auto const& tag, auto& vec, int field_index, int array_dim) {
+                vec.shrink_to_fit();
+            });
+    }
+
   private:
     /**
      * @brief Remove the @f$i^{\text{th}}@f$ row from the container.

src/neuron/model_data.hpp

@@ -117,6 +117,13 @@ struct Model {
     [[nodiscard]] std::unique_ptr<container::utils::storage_info> find_container_info(
         void const* cont) const;
 
+    void shrink_to_fit() {
+        m_node_data.shrink_to_fit();
+        apply_to_mechanisms([](auto& mech_data) { mech_data.shrink_to_fit(); });
+
+        m_identifier_ptrs_for_deferred_deletion.shrink_to_fit();
+    }
+
   private:
     container::Mechanism::storage& mechanism_data_impl(int type) const {
         if (0 <= type && type >= m_mech_data.size()) {

src/nrniv/cxprop.cpp

@@ -2,6 +2,7 @@
 #include "hocdec.h"      // Datum
 #include "section.h"     // Section
 #include "structpool.h"  // Pool
+#include "../neuron/model_data.hpp"
 
 #include <memory>
 #include <vector>
@@ -111,6 +112,7 @@ void nrn_poolshrink(int shrink) {
                 pdatum.reset();
             }
         }
+        neuron::model().shrink_to_fit();
     } else {
         Printf("poolshrink --- type name (dbluse, size) (datumuse, size)\n");
         for (auto i = 0; i < datumpools().size(); ++i) {

src/nrnpython/nrnpy_nrn.cpp

@@ -2223,8 +2223,7 @@ static int rv_setitem(PyObject* self, Py_ssize_t ix, PyObject* value) {
         return -1;
     }
     int err;
-    // Bug that ix is not passed as the last argument?
-    auto const d = nrnpy_rangepointer(sec, r->sym_, r->pymech_->pyseg_->x_, &err, 0 /* idx */);
+    auto const d = nrnpy_rangepointer(sec, r->sym_, r->pymech_->pyseg_->x_, &err, ix);
     if (!d) {
         rv_noexist(sec, r->sym_->name, r->pymech_->pyseg_->x_, err);
         return -1;
@@ -2244,7 +2243,6 @@ static int rv_setitem(PyObject* self, Py_ssize_t ix, PyObject* value) {
                        neuron::container::data_handle<double>{neuron::container::do_not_search, &x},
                        0);
     } else {
-        assert(ix == 0);  // d += ix;
         if (!PyArg_Parse(value, "d", static_cast<double const*>(d))) {
             PyErr_SetString(PyExc_ValueError, "bad value");
             return -1;

test/hoctests/vardimtests/test2.py

@@ -34,3 +34,30 @@
 h("""objref oarray[4][4]""")
 # cannot reach line we want because of earlier array check
 expect_err("h.oarray[2] = []")
+
+
+# test assignment/evaluation of mod file array variable from python
+s = h.Section()
+s.nseg = 3
+s.insert("atst")
+for seg in s:
+    ar = seg.atst.arrayrng
+    assert len(ar) == 4
+    for i in range(len(ar)):
+        ar[i] = i + seg.x
+        seg.arrayrng_atst[i] = ar[i]
+for seg in s:
+    ar = seg.atst.arrayrng
+    for i in range(len(ar)):
+        assert ar[i] == i + seg.x
+        assert seg.arrayrng_atst[i] == i + seg.x
+
+ar = s.arrayrng_atst
+assert len(ar) == 4
+for i in range(len(ar)):
+    ar[i] = i
+for i in range(len(ar)):
+    assert ar[i] == float(i)
+
+expect_err("print(ar[10])")
+expect_err("ar[10] = 1")

test/unit_tests/container/node.cpp

@@ -258,6 +258,7 @@ std::tuple<std::vector<::Node>, std::vector<double>> get_nodes_and_reference_vol
 }  // namespace neuron::test
 
 TEST_CASE("SOA-backed Node structure", "[Neuron][data_structures][node]") {
+    REQUIRE(neuron::model().node_data().size() == 0);
     GIVEN("A default-constructed node") {
         ::Node node{};
         THEN("Check its SOA-backed members have their default values") {
@@ -443,9 +444,12 @@ TEST_CASE("SOA-backed Node structure", "[Neuron][data_structures][node]") {
             }
         }
     }
+    REQUIRE(neuron::model().node_data().size() == 0);
 }
 
 TEST_CASE("Fast membrane current storage", "[Neuron][data_structures][node][fast_imem]") {
+    REQUIRE(neuron::model().node_data().size() == 0);
+
     auto const set_fast_imem = [](bool new_value) {
         nrn_use_fast_imem = new_value;
         nrn_fast_imem_alloc();
@@ -467,6 +471,7 @@ TEST_CASE("Fast membrane current storage", "[Neuron][data_structures][node][fast
     GIVEN("fast_imem calculation is disabled") {
         set_fast_imem(false);
         WHEN("A node is default-constructed") {
+            REQUIRE(neuron::model().node_data().size() == 0);
             ::Node node{};
             check_throws(node);
             auto handle = node.sav_rhs_handle();